Summary: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 Provide feedback
Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II . This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA . The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction .
Todone F, Brick P, Werner F, Weinzierl RO, Onesti S; , Mol Cell 2001;8:1137-1143.: Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex. PUBMED:11741548 EPMC:11741548
Yuan X, Zhao J, Zentgraf H, Hoffmann-Rohrer U, Grummt I; , 0;0:1-2.: Multiple interactions between RNA polymerase I, TIF-IA and TAFI subunits regulate preinitiation complex assembly at the ribosomal gene promoter. PUBMED:12393749 EPMC:12393749
Anantharaman V, Aravind L;, Proteins. 2004;56:795-807.: The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. PUBMED:15281131 EPMC:15281131
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005576
The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [PUBMED:11741548].
This entry represents the N-terminal, heterodimerisation domain of RPB7.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||DNA-directed RNA polymerase activity (GO:0003899)|
|Biological process||transcription, DNA-dependent (GO:0006351)|
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SHS2 is a novel domain with a simple fold containing a core of 3 strands, forming a curved sheet, and a single helix in a strand-helix-strand-strand (SHS2) configuration . SHS2 is found in the bacterial cell division ATPase FtsA, the archaeo-eukaryotic RNA polymerase subunit Rpb7p, the GyrI superfamily, and the uncharacterized MTH1598/Tm1083-like proteins . The fold exists as single copy versions in FtsA (where it is inserted into the RNAseH fold), Rbp7p and Dodecin . It is found as a diad in the GyrI superfamily. In MTH1598/Tm1083-like proteins two copies of SHS2 are found with one inserted into another . The single-copy versions in FtsA and Rbp7 mediate proteinprotein interactions, while the one in Dodecin is a small molecule binding domain. The GyrI also binds small molecule, while the MTH1598 is predicted to be enzymatic .
The clan contains the following 7 members:Archease Cass2 Dodecin GyrI-like SHS2_FTSA SHS2_Rpb7-N SOUL
We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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Curation and family details
|Author:||Finn RD, Anantharaman V|
|Number in seed:||145|
|Number in full:||1033|
|Average length of the domain:||71.80 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||30.62 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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There are 5 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SHS2_Rpb7-N domain has been found. There are 64 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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